HTML widgets blank

[Ben.Tatman@…]

The following bug report has been submitted:
Platform:        Linux-5.14.9-300.fc35.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.3.dev202110020016 (2021-10-02 00:16:37 UTC)
Description
Hi,

On Fedora 35 the initial page with icons showing recently opened files and the log do not show any content. I've attached a screenshot showing the empty log. Also, the About ChimeraX dialog is empty.

I've tried deleting the cache (.cache/ChimeraX), config (.config/ChimeraX) and local/share (.local/share/ChimeraX). I've tried this on both the latest daily build (not sure of version number as I can't open About ChimeraX) as well as the current release (1.2.5-1) and both show the same issue. 

I suspect it's probably a missing library that ChimeraX isn't bundled with that no longer comes with Fedora? Passing the --debug and --devel flags to chimerax-daily doesn't show any error messages other than 

"Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway."

which I had previously on Fedora 34 (and there everything worked).

Thank you,

Ben

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.3.dev202110020016 (2021-10-02)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2qmt

Summary of feedback from opening 2qmt fetched from pdb  
---  
notes | /usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/fetch.py:332: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
system = f"{system} {' '.join(distro.linux_distribution())}"  
Fetching compressed mmCIF 2qmt from http://files.rcsb.org/download/2qmt.cif  
Fetching CCD PO4 from http://ligand-expo.rcsb.org/reports/P/PO4/PO4.cif  
Fetching CCD MRD from http://ligand-expo.rcsb.org/reports/M/MRD/MRD.cif  
Fetching CCD IPA from http://ligand-expo.rcsb.org/reports/I/IPA/IPA.cif  
  
2qmt title:  
Crystal Polymorphism of Protein GB1 Examined by Solid-state NMR and X-ray
Diffraction [more info...]  
  
Chain information for 2qmt #1  
---  
Chain | Description | UniProt  
A | Immunoglobulin G-binding protein G | SPG2_STRSG  
  
Non-standard residues in 2qmt #1  
---  
IPA — isopropyl alcohol (2-propanol)  
MRD — (4R)-2-methylpentane-2,4-diol  
PO4 — phosphate ion  
  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/geometry/matrix.py:121: DeprecationWarning: `np.float` is a
deprecated alias for the builtin `float`. To silence this warning, use `float`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.float64` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import array, zeros, float  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:718: ResourceWarning:
unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/sys_vendor'
mode='r' encoding='utf-8'>  
vendor = open(dmi_prefix + "sys_vendor", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:723: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/sys/devices/virtual/dmi/id/product_name' mode='r' encoding='utf-8'>  
product = open(dmi_prefix + "product_name", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:730: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
OS: {' '.join(distro.linux_distribution())}  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/geometry/matrix.py:121: DeprecationWarning: `np.float` is a
deprecated alias for the builtin `float`. To silence this warning, use `float`
by itself. Doing this will not modify any behavior and is safe. If you
specifically wanted the numpy scalar type, use `np.float64` here.  
Deprecated in NumPy 1.20; for more details and guidance:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations  
from numpy import array, zeros, float  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:718: ResourceWarning:
unclosed file <_io.TextIOWrapper name='/sys/devices/virtual/dmi/id/sys_vendor'
mode='r' encoding='utf-8'>  
vendor = open(dmi_prefix + "sys_vendor", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:723: ResourceWarning:
unclosed file <_io.TextIOWrapper
name='/sys/devices/virtual/dmi/id/product_name' mode='r' encoding='utf-8'>  
product = open(dmi_prefix + "product_name", encoding='utf-8').read().strip()  
ResourceWarning: Enable tracemalloc to get the object allocation traceback  
/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py:730: DeprecationWarning:
distro.linux_distribution() is deprecated. It should only be used as a
compatibility shim with Python's platform.linux_distribution(). Please use
distro.id(), distro.version() and distro.name() instead.  
OS: {' '.join(distro.linux_distribution())}  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.3
OpenGL renderer: Mesa Intel(R) UHD Graphics (ICL GT1)
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 81YH
OS: Fedora Linux 35 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.4Gi       3.4Gi       190Mi       735Mi       3.9Gi       3.1Gi
	Swap:          7.4Gi       5.0Mi       7.4Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Iris Plus Graphics G1 (Ice Lake) [8086:8a56] (rev 07)	
	Subsystem: Lenovo Device [17aa:3f0a]	
	Kernel driver in use: i915
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1
    charset-normalizer: 2.0.6
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.30.1
    ChimeraX-AtomicLibrary: 4.1.4
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202110020016
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.1
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.1
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2
    ChimeraX-ModelPanel: 1.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.2
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.10.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.4.0
    html2text: 2020.1.16
    idna: 3.2
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.8.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.7.3
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.20
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.2
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.0
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: chimeraxlog.png

chimeraxlog.png​

[Ben.Tatman@…]

Added by email2trac

[Greg Couch]

For reference, this issue is fixed by having the appropriate graphics driver installed. Very rarely, an upgrade breaks things and the graphics driver will need to be temporarily downgraded.